/***************************************************************************
 *   Copyright (C) 2007 by Alexandre Masselot,,,   *
 *   alex@alex-laptop   *
 *                                                                         *
 *   This program is free software; you can redistribute it and/or modify  *
 *   it under the terms of the GNU Library General Public License as       *
 *   published by the Free Software Foundation; either version 2 of the    *
 *   License, or (at your option) any later version.                       *
 *                                                                         *
 *   This program is distributed in the hope that it will be useful,       *
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of        *
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
 *   GNU General Public License for more details.                          *
 *                                                                         *
 *   You should have received a copy of the GNU Library General Public     *
 *   License along with this program; if not, write to the                 *
 *   Free Software Foundation, Inc.,                                       *
 *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
 ***************************************************************************/
#ifndef PEPTIDEPMFFACTORY_H
#define PEPTIDEPMFFACTORY_H

#include "peptidefactory.h"
#include "peptidepmf.h"

/**
  A factory to transform stream PeptidePMF

  Limit (current):
     * only one fix modification to be assigned per amino acid
     * each amino acid can only have one combination of PTM (it is not possible to have all the M with oxidation variable, and one specific of them with an annotated di-methyl for example)

	@author Alexandre Masselot,,, <alex@alex-laptop>
*/
namespace bol{
class PeptidePMFFactory: public PeptideFactory{
private:
    int m_charCounterInit[29];
    int m_charCounter[29];
    unsigned char m_fixAAMapping[29];
    unsigned char *m_varAAMapping[29];

public:
    /**
     * default constructor (just setup working buffers)
     */
    PeptidePMFFactory();

    ~PeptidePMFFactory();

    void setPeptideModifier(PeptideModifier* theValue);
    /**
     * based on set modificationin the modifier and a given peptide, fills in a vector of PMF peptides
     * @param src the basic peptide
     * @param vpept the vector to be filled (is it not cleared by this method)
     */
    void createPeptides(Peptide& src, vector<PeptidePMF>& vpept);

};
}
#endif
